Pakistan's military has escalated its brutal campaign of abduction and extra-judicial execution targeting nationalist rebels in Balochistan province, human rights groups have said.

In a new report on "enforced disappearances" by military and intelligence officials, Human Rights Watch (HRW) criticised the failure of Pakistan's civilian leaders to halt what it termed a human rights "free-for-all".

"The national government has done little to end the carnage," said HRW's Asia director, Brad Adams. "President Asif Ali Zardari has to realise it cannot just be wished away."

Covered in desert, mineral-rich and strategically located between Iran and Afghanistan, Balochistan is home to some of the most brutal state-led human rights abuses in Pakistan.

Suspected nationalist rebels or sympathisers are routinely picked up in broad daylight, taken to centres where torture is rife and, in an increasing number of cases, later found dead on the roadside with a bullet wound in the head.

Local groups have counted more than 180 bodies, mostly of men who reportedly disappeared at the hands of the Inter-Services Intelligence agency (ISI) in co-operation with Frontier Corps paramilitaries.

The military leadership is accused of orchestrating the violence as it seeks to crush a small rebel force it believes is being covertly boosted by arch-rival India – an accusation some western spies say is true.

The nationalists are also guilty of gross human rights violations, in particularly the targeted killing of Punjabi "settlers", teachers, politicians and anyone deemed to be co-operating with the military.

A sense of lawlessness and impunity reigns in the province, which covers 43% of Pakistan's land mass but accounts for just 5% of the population. One former detainee said his captors told him: "We can torture you, or kill you, or keep you for years at our will. It is only the army chief and the [intelligence] chief that we obey."

Army spokesman Major General Athar Abbas said the accusations were false. "We've responded to all this before. It's basically untrue," he said.

Conflict in the western province receives relatively little attention because unlike the Taliban, Baloch rebels have secular politics and pose little serious threat to the army.

Pakistani security officials estimate there are just 1,000 nationalist fighters, whose leaders are largely exiled in the UK, Switzerland and Dubai. But analysts say the barbarity underscores the fragility of Pakistani unity and could be a harbinger of unrest elsewhere.

The rebels want independence from Pakistan, saying that after decades of neglect from the centre they would be better off on their own.

The fighting is small-scale: rebels attack electricity pylons, rail tracks and military convoys; the military responds by detaining those thought to be responsible.

HRW says that in military detention camps, prisoners are beaten, hung upside down and deprived of food and sleep for long periods. Over the past year the bodies of detainees have turned up on the roadside across the province, triggering protests in the provincial capital, Quetta.

The exact number of those detained is unclear. In 2008 the interior minister, Rehman Malik, said at least 1,100 people were missing, but last January the Balochistan home minister put the figure at just 55 people.

Targeted killings of "settlers" and other accused collaborators by rebels is carving up the province along worrisome ethnic lines – in Quetta, for instance, non-Baloch doctors refused to work in Baloch areas, fearing harm.

The Zardari government has tried to appease nationalist sentiment through a generous aid package and greater funding, but the disappearances and deaths have fuelled nationalist sentiment.

A supreme court judge said last year that disappearances from Balochistan posed "the most burning issue in the country". But a judicial enquiry into the matter has been largely toothless due to a lack of military co-operation.